The current challenge for world agriculture is to provide food for a growing population, within a context of environmental degradation and economic inequality. The challenge is how to produce accessible, healthy, diverse, nutritious, safe and abundant food in a way that is sustainable, allowing farmers to exert food sovereignty while at the same time addressing ecosystem conservation. The aim of this study is to explore the potential contribution of traditional agriculture to food sovereignty and also to understand the challenges that indigenous communities are facing today. Our case studies are from six Latin-American countries: Chile, Peru, Ecuador, Colombia, Guatemala and Mexico, where we carried out semi-structured, guided visits and field observations. Our results shed light on how traditional agricultural knowledge, techniques and practices can contribute to these issues, but also to the need of protecting and recovering the cultural and ecological heritage. There is a need to resolve public management issues, related to development investment, technological packages, cultural loss and gender. If these are not addressed, the potential contribution of ancient agricultural knowledge will fail to contribute to strengthen food sovereignty and maintain the local markets, which are also places for seed exchange, knowledge sharing and social networking.